Fluorine in PDB 7nbk: Solution Structure of Dna Duplex Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification

The binding sites of Fluorine atom in the Solution Structure of Dna Duplex Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification (pdb code 7nbk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Solution Structure of Dna Duplex Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification, PDB code: 7nbk:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Solution Structure of Dna Duplex Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Solution Structure of Dna Duplex Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification within 5.0Å range: probe atom residue distance (Å) B Occ A:F5 b:0.0 occ:1.00 F1 A:U7B5 0.0 0.0 1.0 C2' A:U7B5 1.4 0.0 1.0 F2 A:U7B5 2.3 0.0 1.0 C1' A:U7B5 2.3 0.0 1.0 H1' A:U7B5 2.4 0.0 1.0 C3' A:U7B5 2.5 0.0 1.0 H8 A:DG6 2.7 0.0 1.0 O3' A:U7B5 2.8 0.0 1.0 H5' A:DG6 2.8 0.0 1.0 O5' A:DG6 2.8 0.0 1.0 C8 A:DG6 2.9 0.0 1.0 O2 A:U7B5 3.2 0.0 1.0 C5' A:DG6 3.2 0.0 1.0 H3' A:U7B5 3.3 0.0 1.0 N1 A:U7B5 3.3 0.0 1.0 H4' A:U7B5 3.3 0.0 1.0 O4' A:DG6 3.3 0.0 1.0 C4' A:U7B5 3.3 0.0 1.0 P A:DG6 3.3 0.0 1.0 O4' A:U7B5 3.4 0.0 1.0 N9 A:DG6 3.4 0.0 1.0 N7 A:DG6 3.5 0.0 1.0 C2 A:U7B5 3.6 0.0 1.0 OP2 A:DG6 3.7 0.0 1.0 C4' A:DG6 3.9 0.0 1.0 C1' A:DG6 3.9 0.0 1.0 C5 A:DG6 4.2 0.0 1.0 C4 A:DG6 4.2 0.0 1.0 H5'' A:DG6 4.2 0.0 1.0 H2' A:DG6 4.3 0.0 1.0 C6 A:U7B5 4.3 0.0 1.0 H21 B:DG8 4.3 0.0 1.0 H6 A:U7B5 4.6 0.0 1.0 H4' A:DG6 4.6 0.0 1.0 C2' A:DG6 4.6 0.0 1.0 OP1 A:DG6 4.6 0.0 1.0 C5' A:U7B5 4.8 0.0 1.0 N3 A:U7B5 4.8 0.0 1.0 H1' A:DG6 4.8 0.0 1.0 C3' A:DG6 4.9 0.0 1.0

Fluorine binding site 2 out of 4 in the Solution Structure of Dna Duplex Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Solution Structure of Dna Duplex Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification within 5.0Å range: probe atom residue distance (Å) B Occ A:F5 b:0.0 occ:1.00 F2 A:U7B5 0.0 0.0 1.0 C2' A:U7B5 1.4 0.0 1.0 F1 A:U7B5 2.3 0.0 1.0 H3' A:U7B5 2.4 0.0 1.0 C3' A:U7B5 2.4 0.0 1.0 C1' A:U7B5 2.4 0.0 1.0 N1 A:U7B5 2.7 0.0 1.0 H8 A:DG6 2.9 0.0 1.0 C6 A:U7B5 3.0 0.0 1.0 H6 A:U7B5 3.1 0.0 1.0 N7 A:DG6 3.1 0.0 1.0 O4' A:U7B5 3.2 0.0 1.0 C8 A:DG6 3.2 0.0 1.0 H1' A:U7B5 3.3 0.0 1.0 OP2 A:DG6 3.3 0.0 1.0 C4' A:U7B5 3.4 0.0 1.0 O3' A:U7B5 3.4 0.0 1.0 C2 A:U7B5 3.5 0.0 1.0 P A:DG6 3.8 0.0 1.0 O2 A:U7B5 3.9 0.0 1.0 O5' A:DG6 4.0 0.0 1.0 C5 A:U7B5 4.0 0.0 1.0 H4' A:U7B5 4.0 0.0 1.0 C5 A:DG6 4.3 0.0 1.0 N3 A:U7B5 4.4 0.0 1.0 N9 A:DG6 4.4 0.0 1.0 O5' A:U7B5 4.5 0.0 1.0 C5' A:U7B5 4.5 0.0 1.0 C4 A:U7B5 4.6 0.0 1.0 H2'' A:DA4 4.6 0.0 1.0 H5 A:U7B5 4.6 0.0 1.0 H5' A:DG6 4.7 0.0 1.0 C4 A:DG6 4.9 0.0 1.0 C5' A:DG6 5.0 0.0 1.0

Fluorine binding site 3 out of 4 in the Solution Structure of Dna Duplex Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Solution Structure of Dna Duplex Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification within 5.0Å range: probe atom residue distance (Å) B Occ B:F11 b:0.0 occ:1.00 F1 B:U7B11 0.0 0.0 1.0 C2' B:U7B11 1.4 0.0 1.0 F2 B:U7B11 2.3 0.0 1.0 H1' B:U7B11 2.4 0.0 1.0 C1' B:U7B11 2.4 0.0 1.0 C3' B:U7B11 2.5 0.0 1.0 O3' B:U7B11 2.8 0.0 1.0 H5' B:DG12 2.9 0.0 1.0 O5' B:DG12 2.9 0.0 1.0 H8 B:DG12 2.9 0.0 1.0 C8 B:DG12 2.9 0.0 1.0 H3' B:U7B11 3.2 0.0 1.0 N1 B:U7B11 3.3 0.0 1.0 H4' B:U7B11 3.3 0.0 1.0 N9 B:DG12 3.3 0.0 1.0 C4' B:U7B11 3.3 0.0 1.0 N7 B:DG12 3.3 0.0 1.0 P B:DG12 3.4 0.0 1.0 C5' B:DG12 3.4 0.0 1.0 O2 B:U7B11 3.4 0.0 1.0 O4' B:U7B11 3.4 0.0 1.0 O4' B:DG12 3.5 0.0 1.0 C2 B:U7B11 3.7 0.0 1.0 OP2 B:DG12 3.7 0.0 1.0 C5 B:DG12 3.8 0.0 1.0 C4 B:DG12 3.8 0.0 1.0 C1' B:DG12 3.9 0.0 1.0 C4' B:DG12 4.0 0.0 1.0 H5'' B:DG12 4.3 0.0 1.0 C6 B:U7B11 4.3 0.0 1.0 H2' B:DG12 4.4 0.0 1.0 H6 B:U7B11 4.5 0.0 1.0 OP1 B:DG12 4.7 0.0 1.0 H21 A:DG2 4.7 0.0 1.0 C2' B:DG12 4.7 0.0 1.0 C5' B:U7B11 4.8 0.0 1.0 N3 B:DG12 4.8 0.0 1.0 H4' B:DG12 4.8 0.0 1.0 C6 B:DG12 4.8 0.0 1.0 H1' B:DG12 4.8 0.0 1.0 N3 B:U7B11 4.9 0.0 1.0

Fluorine binding site 4 out of 4 in the Solution Structure of Dna Duplex Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Solution Structure of Dna Duplex Containing A 2'-Deoxy-2'2'- Difluorodeoxycytidine (Gemcitabine) Modification within 5.0Å range: probe atom residue distance (Å) B Occ B:F11 b:0.0 occ:1.00 F2 B:U7B11 0.0 0.0 1.0 C2' B:U7B11 1.4 0.0 1.0 F1 B:U7B11 2.3 0.0 1.0 H3' B:U7B11 2.4 0.0 1.0 C3' B:U7B11 2.4 0.0 1.0 C1' B:U7B11 2.4 0.0 1.0 N1 B:U7B11 2.7 0.0 1.0 H6 B:U7B11 3.0 0.0 1.0 C6 B:U7B11 3.0 0.0 1.0 N7 B:DG12 3.0 0.0 1.0 H8 B:DG12 3.1 0.0 1.0 O4' B:U7B11 3.2 0.0 1.0 C8 B:DG12 3.2 0.0 1.0 H1' B:U7B11 3.3 0.0 1.0 OP2 B:DG12 3.3 0.0 1.0 C4' B:U7B11 3.4 0.0 1.0 O3' B:U7B11 3.4 0.0 1.0 C2 B:U7B11 3.6 0.0 1.0 P B:DG12 3.8 0.0 1.0 O5' B:DG12 4.0 0.0 1.0 C5 B:U7B11 4.0 0.0 1.0 C5 B:DG12 4.0 0.0 1.0 H4' B:U7B11 4.0 0.0 1.0 O2 B:U7B11 4.1 0.0 1.0 N9 B:DG12 4.3 0.0 1.0 N3 B:U7B11 4.5 0.0 1.0 H2'' B:DA10 4.5 0.0 1.0 C5' B:U7B11 4.6 0.0 1.0 O5' B:U7B11 4.6 0.0 1.0 C4 B:U7B11 4.7 0.0 1.0 H5 B:U7B11 4.7 0.0 1.0 C4 B:DG12 4.7 0.0 1.0 H5' B:DG12 4.8 0.0 1.0 C6 B:DG12 4.8 0.0 1.0 O6 B:DG12 5.0 0.0 1.0

C.Cabrero, N.Martin-Pintado, S.Mazzini, R.Gargallo, R.Eritja, A.Avino, C.Gonzalez. Structural Effects of Incorporation of 2 -Deoxy-2 2 -Difluorodeoxycytidine (Gemcitabine) in A- and B-Form Duplexes. Chemistry 2021.
ISSN: ISSN 0947-6539
PubMed: 33772916
DOI: 10.1002/CHEM.202100503